Locus 2546

Sequence ID 2R_DroMel_CAF1
Location 9,061,007 – 9,061,180
Length 173
Max. P 0.775864
window4188 window4189

overview

Window 8

Location 9,061,007 – 9,061,113
Length 106
Sequences 5
Columns 107
Reading direction reverse
Mean pairwise identity 78.22
Mean single sequence MFE -31.16
Consensus MFE -12.30
Energy contribution -14.74
Covariance contribution 2.44
Combinations/Pair 1.12
Mean z-score -2.10
Structure conservation index 0.39
SVM decision value 0.54
SVM RNA-class probability 0.775864
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9061007 106 - 20766785
GCACUUU-GUUGGCAUGCCACUAGUUAACGUUAACGUUAACGUUAACGCUGUUUUCUAGCGCACACAUGACUUGGCAUUUCUGGGCUCCGAGCCGCAAGCCCACUUU
.......-((.(((((((((..(((((..(((((((....)))))))((((.....)))).......)))))))))))...(((((.....))).)).))).))... ( -33.20)
>DroSec_CAF1 26244 99 - 1
GCACUUU-GUUGGCA-GCCACUAGUUAACGUUAACGUUAG------CGUUGUUUUCUAGCGCACACAUGACUUGGCAUUUCUGGGCUCCGAGGCCCAAGCCCACUUU
.......-((.(((.-((((..((((((((....)))).(------(((((.....))))))......)))))))).....((((((....)))))).))).))... ( -32.50)
>DroSim_CAF1 28316 99 - 1
GCACUCU-GUUGGCA-GCCACUGGUUAACGUUAACGUUAG------CGUUGUUUUCUAGCGCACACAUGACUUGGCAUUUCUGGGCUCCGAGCCCCAAGCCCACUUU
.......-((.(((.-((((..((((((((....)))).(------(((((.....))))))......))))))))......((((.....))))...))).))... ( -30.20)
>DroYak_CAF1 28093 84 - 1
GCACUUU-GUUGGCA-GCCACUGGUCAACG---------------------UUUUCUAGCGCAGACAUGACUUGGCAUUUCUGGGCUCCAAGCCCCAAGCCCACUUU
.......-((.(((.-((((..(((((..(---------------------(((.(....).)))).)))))))))......((((.....))))...))).))... ( -24.70)
>DroAna_CAF1 30782 96 - 1
GUACUUUUGAUAGCGAGCCG--AGCUU-CAGUA-GCUUAG------CUGGCUUUUCUAGUGCAGACAUGACUUGGCAUUUGUGGGGUCUGGGCCCCAA-CCCACUUU
(((((...((.(((.(((..--((((.-....)-)))..)------)).)))..)).)))))..........(((......((((((....)))))).-.))).... ( -35.20)
>consensus
GCACUUU_GUUGGCA_GCCACUAGUUAACGUUAACGUUAG______CGUUGUUUUCUAGCGCACACAUGACUUGGCAUUUCUGGGCUCCGAGCCCCAAGCCCACUUU
........((.(((..((((..(((((.......((((((...............))))))......))))))))).....((((........)))).))).))... (-12.30 = -14.74 +   2.44)

alignment

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secondary structure

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dotplot

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Window 9

Location 9,061,074 – 9,061,180
Length 106
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 81.77
Mean single sequence MFE -25.98
Consensus MFE -17.54
Energy contribution -18.02
Covariance contribution 0.48
Combinations/Pair 1.15
Mean z-score -1.44
Structure conservation index 0.68
SVM decision value 0.01
SVM RNA-class probability 0.538382
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9061074 106 - 20766785
---AAGCUU--CGCCUUGGCUCGAGCUAGUGCUAAGGAGAAAAUAAAACAGAUUAUAUAACGUGUAAUUAGAGCACUUU-GUUGGCAUGCCACUAGUUAACGUUAACGUUAA
---.(((((--(.(((((((.(......).))))))).)))................((((((.((((((((((.....-)))((....)).)))))))))))))..))).. ( -27.20)
>DroSec_CAF1 26305 105 - 1
---AAGCUU--CGCCUUGGCUCGAGCUAGUGCUAAGGAGAAAAUAAAACAGAUUAUAUAACGUGUAAUUAGAGCACUUU-GUUGGCA-GCCACUAGUUAACGUUAACGUUAG
---.(((((--(.(((((((.(......).))))))).)))................((((((.(((((((.((.((..-...))..-))..)))))))))))))..))).. ( -25.00)
>DroSim_CAF1 28377 105 - 1
---AAGCUU--CGCCUUGGCUCGAGCUAGUGCUAAGGAGAAAAUAAAACAGAUUAUAUAACGUGUAAUUAGAGCACUCU-GUUGGCA-GCCACUGGUUAACGUUAACGUUAG
---......--.(((.((((((.(((.((((((..(............).((((((((...))))))))..))))))..-))).).)-))))..)))(((((....))))). ( -26.90)
>DroEre_CAF1 31969 95 - 1
---AAGCUU--UGCCUUGGCUCGAGCUGGUGCUAAGGAGAAAAUAAAACAGAUUAUAUAACGUGUAAUUAGAGCACUUU-GCUGGCA-GCCACUGCUUAACG----------
---......--.((..((((((.(((.((((((..(............).((((((((...))))))))..))))))..-))).).)-))))..))......---------- ( -25.00)
>DroYak_CAF1 28149 95 - 1
---GAGCUU--UACCUUGGCUCGAGCUGGUGCUAAGGAGAAAAUAAAACAGAUUAUAUAACGUGUAAUUAGAGCACUUU-GUUGGCA-GCCACUGGUCAACG----------
---..((((--(.(((((((.(......).))))))).............((((((((...))))))))))))).....-((((((.-.......)))))).---------- ( -25.40)
>DroAna_CAF1 30842 108 - 1
AAAAAAAUUCCAGCCUUGGCUCGCGUCUGUGCUAAAAAGAAAAUAAAAGCGAUUAUAUAACGUGUAAUUAGAGUACUUUUGAUAGCGAGCCG--AGCUU-CAGUA-GCUUAG
...........(((.((((((((((((.(((((.................((((((((...))))))))..)))))....))).))))))))--)))).-.....-...... ( -26.41)
>consensus
___AAGCUU__CGCCUUGGCUCGAGCUAGUGCUAAGGAGAAAAUAAAACAGAUUAUAUAACGUGUAAUUAGAGCACUUU_GUUGGCA_GCCACUAGUUAACGUUA_CGUUAG
.....((((....(((((((.(......).))))))).............((((((((...)))))))).))))......((((((.........))))))........... (-17.54 = -18.02 +   0.48)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:32:38 2006